Package picard.arrays.illumina
Enum Build37ExtendedIlluminaManifestRecord.Flag
- java.lang.Object
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- java.lang.Enum<Build37ExtendedIlluminaManifestRecord.Flag>
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- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
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- All Implemented Interfaces:
Serializable
,Comparable<Build37ExtendedIlluminaManifestRecord.Flag>
- Enclosing class:
- Build37ExtendedIlluminaManifestRecord
protected static enum Build37ExtendedIlluminaManifestRecord.Flag extends Enum<Build37ExtendedIlluminaManifestRecord.Flag>
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Enum Constant Summary
Enum Constants Enum Constant Description DUPE
The record passes validation but is a duplicate (another assay at the same locus with the same alleles)ILLUMINA_FLAGGED
Flagged by Illumina as a bad assayINDEL_CONFLICT
Both insertion and deletion sequence found in reference.INDEL_EXTENSION_ERROR
Deprecated.- but used in existing extended manifest files.INDEL_NOT_FOUND
Neither insertion nor deletion sequence found in reference.INDEL_SEQ_MISMATCH
Deprecated.- but used in existing extended manifest files.LIFTOVER_FAILED
MISSING_ALLELE_B_PROBESEQ
Manifest contained no allele B probe sequencePASS
The record in the manifest passes validation and will be used in VCF generationPROBE_SEQUENCE_MISMATCH
Probe sequence not found in reference.PROBE_SEQUENCE_STRAND_INVALID
Deprecated.- but used in existing extended manifest files.SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files.SOURCE_SEQUENCE_INVALID
Source sequence is invalid (contains invalid character).SOURCE_SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files.SOURCE_SEQUENCE_STRAND_INVALID
Deprecated.- but used in existing extended manifest files.UNSUPPORTED_GENOME_BUILD
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static Build37ExtendedIlluminaManifestRecord.Flag
valueOf(String name)
Returns the enum constant of this type with the specified name.static Build37ExtendedIlluminaManifestRecord.Flag[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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PASS
public static final Build37ExtendedIlluminaManifestRecord.Flag PASS
The record in the manifest passes validation and will be used in VCF generation
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DUPE
public static final Build37ExtendedIlluminaManifestRecord.Flag DUPE
The record passes validation but is a duplicate (another assay at the same locus with the same alleles)
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ILLUMINA_FLAGGED
public static final Build37ExtendedIlluminaManifestRecord.Flag ILLUMINA_FLAGGED
Flagged by Illumina as a bad assay
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LIFTOVER_FAILED
public static final Build37ExtendedIlluminaManifestRecord.Flag LIFTOVER_FAILED
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UNSUPPORTED_GENOME_BUILD
public static final Build37ExtendedIlluminaManifestRecord.Flag UNSUPPORTED_GENOME_BUILD
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PROBE_SEQUENCE_MISMATCH
public static final Build37ExtendedIlluminaManifestRecord.Flag PROBE_SEQUENCE_MISMATCH
Probe sequence not found in reference.
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MISSING_ALLELE_B_PROBESEQ
public static final Build37ExtendedIlluminaManifestRecord.Flag MISSING_ALLELE_B_PROBESEQ
Manifest contained no allele B probe sequence
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SOURCE_SEQUENCE_INVALID
public static final Build37ExtendedIlluminaManifestRecord.Flag SOURCE_SEQUENCE_INVALID
Source sequence is invalid (contains invalid character).
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INDEL_NOT_FOUND
public static final Build37ExtendedIlluminaManifestRecord.Flag INDEL_NOT_FOUND
Neither insertion nor deletion sequence found in reference.
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INDEL_CONFLICT
public static final Build37ExtendedIlluminaManifestRecord.Flag INDEL_CONFLICT
Both insertion and deletion sequence found in reference.
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PROBE_SEQUENCE_STRAND_INVALID
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag PROBE_SEQUENCE_STRAND_INVALID
Deprecated.- but used in existing extended manifest files.
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SOURCE_SEQUENCE_MISMATCH
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag SOURCE_SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files.
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SOURCE_SEQUENCE_STRAND_INVALID
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag SOURCE_SEQUENCE_STRAND_INVALID
Deprecated.- but used in existing extended manifest files.
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SEQUENCE_MISMATCH
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag SEQUENCE_MISMATCH
Deprecated.- but used in existing extended manifest files.
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INDEL_SEQ_MISMATCH
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag INDEL_SEQ_MISMATCH
Deprecated.- but used in existing extended manifest files.
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INDEL_EXTENSION_ERROR
@Deprecated public static final Build37ExtendedIlluminaManifestRecord.Flag INDEL_EXTENSION_ERROR
Deprecated.- but used in existing extended manifest files.
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Method Detail
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values
public static Build37ExtendedIlluminaManifestRecord.Flag[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (Build37ExtendedIlluminaManifestRecord.Flag c : Build37ExtendedIlluminaManifestRecord.Flag.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static Build37ExtendedIlluminaManifestRecord.Flag valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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